Alignments for a candidate for hutH in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Pseudomonas simiae WCS417

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate GFF342 PS417_01745 histidine ammonia-lyase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1582
         (507 letters)



>FitnessBrowser__WCS417:GFF342
          Length = 502

 Score =  851 bits (2198), Expect = 0.0
 Identities = 431/495 (87%), Positives = 461/495 (93%)

Query: 1   MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60
           MSQA KI IADAPLRWQDV AVARHGA LELS Q W RI+NAQAIVQRIV SGERAYGVN
Sbjct: 1   MSQATKITIADAPLRWQDVAAVARHGAVLELSGQAWARIDNAQAIVQRIVTSGERAYGVN 60

Query: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120
           TGLGALCNVSLKGEQLSQLSRNTLLSHACGVG  L+DEQTRAIICAAI NYSHGKSG+H 
Sbjct: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGPVLSDEQTRAIICAAIINYSHGKSGLHP 120

Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180
           +VV +LLALLN GITPQVPSQGSVGYLTHMAH+G+ LLGVG VSY+G+IV AQ+ALS EG
Sbjct: 121 QVVHSLLALLNHGITPQVPSQGSVGYLTHMAHVGVALLGVGTVSYQGRIVPAQEALSAEG 180

Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240
           L PV LGAKDGLCLVNGTPCMTGLSCLA+ADA  L+QWADVIGAMSFEAQRGQI AFD E
Sbjct: 181 LHPVVLGAKDGLCLVNGTPCMTGLSCLALADAHHLLQWADVIGAMSFEAQRGQIDAFDEE 240

Query: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300
           IIALKPH GMQQVGINLRALLDGSEVIASS+GIRTQDALSIRSIPQ+HGAARDQ+EHA +
Sbjct: 241 IIALKPHPGMQQVGINLRALLDGSEVIASSQGIRTQDALSIRSIPQIHGAARDQVEHATR 300

Query: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360
           QIETELNS TDNP++LGTPD++RV+SQANPHGQSVALAAD+LAIAMAEIG++AERRLDRL
Sbjct: 301 QIETELNSATDNPLVLGTPDHYRVVSQANPHGQSVALAADMLAIAMAEIGAVAERRLDRL 360

Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420
           INPHVSGLPAFLV+NPGVNSGMMIVQYVAASLC +NRQLAQPAVLDN+VTSGLQEDHLSM
Sbjct: 361 INPHVSGLPAFLVSNPGVNSGMMIVQYVAASLCGQNRQLAQPAVLDNFVTSGLQEDHLSM 420

Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480
           GTNAALKLH+ L N TQILAIEYLLAAQAFEFLKEQRFGAGTD AWRLLRE VPAY+QDR
Sbjct: 421 GTNAALKLHQVLANVTQILAIEYLLAAQAFEFLKEQRFGAGTDRAWRLLREVVPAYEQDR 480

Query: 481 WLAPDIAAAAGVLKD 495
           WLAPDIAAAA +LKD
Sbjct: 481 WLAPDIAAAAKLLKD 495


Lambda     K      H
   0.319    0.133    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 937
Number of extensions: 28
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 507
Length of database: 502
Length adjustment: 34
Effective length of query: 473
Effective length of database: 468
Effective search space:   221364
Effective search space used:   221364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate GFF342 PS417_01745 (histidine ammonia-lyase)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01225.hmm
# target sequence database:        /tmp/gapView.13636.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine ammonia-lyase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.6e-167  543.2   5.5   3.2e-167  542.9   5.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF342  PS417_01745 histidine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF342  PS417_01745 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.9   5.5  3.2e-167  3.2e-167       2     493 ..       8     497 ..       7     501 .. 0.98

  Alignments for each domain:
  == domain 1  score: 542.9 bits;  conditional E-value: 3.2e-167
                          TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnl 77 
                                        ++    l+ +d++avar++a +els +a +++++++a++++iv++ +  YGvntG G+l +v ++ e+l +L rn 
  lcl|FitnessBrowser__WCS417:GFF342   8 TIADAPLRWQDVAAVARHGAVLELSGQAWARIDNAQAIVQRIVTSGERAYGVNTGLGALCNVSLKGEQLSQLSRNT 83 
                                        666778999******************************************************************* PP

                          TIGR01225  78 vrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalv 153
                                        ++sHa+GvG  l++e +Ra++   +   ++G sg+  +v++ l+alln++++P vp++GsvG    L  +ah++++
  lcl|FitnessBrowser__WCS417:GFF342  84 LLSHACGVGPVLSDEQTRAIICAAIINYSHGKSGLHPQVVHSLLALLNHGITPQVPSQGSVG---YLTHMAHVGVA 156
                                        *************************************************************7...6999******* PP

                          TIGR01225 154 liGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallg 229
                                        l+G G + ++g++++a+eaL a gl+Pv l ak+Gl L+nGt +mt+l +lal+da++ll+ ad+++a+s+ea  g
  lcl|FitnessBrowser__WCS417:GFF342 157 LLGVGTVSYQGRIVPAQEALSAEGLHPVVLGAKDGLCLVNGTPCMTGLSCLALADAHHLLQWADVIGAMSFEAQRG 232
                                        **************************************************************************** PP

                          TIGR01225 230 tskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiEln 305
                                          +afd++i +++ph+g  +v+ +lr ll+gse+  s  +  r qDa s+R+iPq+hGa++d+++++ + +++Eln
  lcl|FitnessBrowser__WCS417:GFF342 233 QIDAFDEEIIALKPHPGMQQVGINLRALLDGSEVIASS-QGIRTQDALSIRSIPQIHGAARDQVEHATRQIETELN 307
                                        *************************************9.778********************************** PP

                          TIGR01225 306 satDnPlvf..adegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlm 379
                                        satDnPlv+  +d+ +vvs  n Hg+ vAla+d+laia+ae+ga++eRR++rl++p+ s+Lp+FL+ ++G+nsG+m
  lcl|FitnessBrowser__WCS417:GFF342 308 SATDNPLVLgtPDHYRVVSQANPHGQSVALAADMLAIAMAEIGAVAERRLDRLINPHVSGLPAFLVSNPGVNSGMM 383
                                        ********83356789************************************************************ PP

                          TIGR01225 380 iaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaekta 455
                                        i qy aA+L+ +n++La+Pa +D+  ts+ qEDH smg+ aa kl +v +nv++++aiE+l+aaq+ ef+k+++  
  lcl|FitnessBrowser__WCS417:GFF342 384 IVQYVAASLCGQNRQLAQPAVLDNFVTSGLQEDHLSMGTNAALKLHQVLANVTQILAIEYLLAAQAFEFLKEQRFG 459
                                        **************************************************************************** PP

                          TIGR01225 456 aelekvyeavRevveeleeDRvlapDleavkellekes 493
                                        a ++++  ++Revv+ +e+DR lapD++a+ +ll++  
  lcl|FitnessBrowser__WCS417:GFF342 460 AGTDRAWRLLREVVPAYEQDRWLAPDIAAAAKLLKDTD 497
                                        **********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (502 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources